Barclay, who is experiencing some form of transporter phobia, speaks to CounselorTroi about his troubles and she introduces him to a relaxation technique known as plexing. However, completely unconvinced and still tapping himself on the neck as he walks out the door he returns to the transporter room, preparing himself for the ride. He's comforted a little by O'Brien, who tells him about his fear of spiders, which he conquered by crawling past twenty Talarian hook spiders.

After collecting fragments, CommandersLa Forge, Data and Lieutenant Barclay beam back to the Enterprise. During transport, Barclay has an awful vision of a worm-like creature swimming in the matter stream and touching his arm. He steps out a changed man, fearful – life will never be the same again. Plagued by what he saw, he is constantly analyzing himself by drinking lots of water and even going so far as to diagnose himself with transporter psychosis. Eventually he seeks out Dr.Crusher. Smiling, Dr. Crusher tells Barclay to stay away from the Starfleet Medical Database, assuring him that he does not have transporter psychosis.

Barclay is suffering from pain, with affected areas of his body lighting up in blue flashes as if they were in the transporter. Barclay ascribes this to his transporter psychosis and keeps quiet about it. Meanwhile, in Engineering, La Forge and Data run tests on the plasma, discovering that it contains quasi-energy microbes. They attempt to recreate conditions on the Yosemite. They first take the precaution of setting up a force field around the container. Once the plasma field is beamed aboard the Enterprise it explodes, though the explosion is contained within the force field. Barclay collapses, and is taken to sickbay. Dr. Crusher discovers that some of the quasi-energy microbes from the Yosemite have gotten into Barclay's bloodstream during transport back to the Enterprise and this is what has been causing him pain, and all the other symptoms.

La Forge and O'Brien decide that the transporter could be used, once proper adjustments were made, to remove the microbes from Barclay's body. Once Barclay is inside the beam, he sees the creepy creatures again. In a spontaneous act of bravery, the lieutenant appears to catch one of the creatures in his arms and doesn't let go. When he rematerializes, we see that he has another person in his grasp, one of the Yosemite crew members. Barclay tells the others that there are three more crew members caught in the matter stream. He sends a security team led by Worf in to save the rest of the Yosemite crew from the transporter. Barclay explains to La Forge and the chief that while the crew of the USS Yosemite was trying to cleanse themselves of the quasi-energy microbes, Human patterns got trapped in the transporter which didn't allow them to escape. Worf and the away team return with the other three members of the Yosemite crew.

O'Brien meets Barclay at Ten Forward, and shows him his pet Lycosa tarantula, whom he adopted after getting over his arachnophobia. He gets up to grab some drinks, while the tarantula crawls up Barclay's arm, who is nervously waiting for O'Brien to return...

"Chief."
"Lieutenant. Glad you could make it. You know, I think this is the first time we've ever spoken outside of the transporter room."
"Well, to be honest, I've always avoided you."
"Why?"
"Because you run the transporters, and I hate the transporters. At least, I used to."

Brannon Braga enjoyed writing this episode. "Certainly, it was one of my most personal episodes. People around here say I am Barclay. I hate flying and that's where the idea came from. If I lived in the 24th century, I'd be afraid to transport, so I enjoyed exploring some of the deeper neuroses that Barclay had." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Michael Piller remarked, "I always like the Barclay shows. I think it's a perfectly valid fear to explore, whether you have a phobia about spiders or about being molecularly taken apart and put back together. As Star Trek viewers we have come to take it for granted, but why shouldn't somebody be afraid to get into a transporter? I had always felt that there were too many similarities to the Twilight Zone where Shatner looks out and sees the creature on the wing of the plane. I felt very strongly we needed to get the episode away from that, and I think we succeeded." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Barclay mentions in this episode that spiders never bothered him. Later, in "Genesis" (also written by Brannon Braga), Barclay would de-evolve into a spider-like creature.

This is the first and only time O'Brien's pet tarantula, Christina, is ever seen or mentioned.

This episode is the first to show a first-person perspective of the transport process; the only other time this was done is in "Prototype".

While expressing his fear of transporting, Barclay asks La Forge, "Commander, has anything strange ever happened to you during transport... anything out of the ordinary?" La Forge answered dismissively, "No, not really." However, in an episode during the previous season, La Forge himself was involved in a transporter malfunction that transported him and Ensign Ro out of phase with the rest of reality. They were reported missing, and presumed dead. They ultimately rematerialized in the midst of their own memorial service. (TNG: "The Next Phase")

Jeri Taylor observed, "This was an episode that a lot of people just didn't respond to and I don't know why. I thought it was a wonderful idea. I thought Brannon wrote a terrific script. It just seemed so perfect, Barclay with a transporter phobia just seemed like a marvelous marriage of something people can relate to today and in the future: technology. I just thought everything worked with the exception of the visual effects. The explanation by the end really got painfully detailed. And it's that fine line you try to draw, if we don't say this, is the audience going to be fairly confused and cheated because they don't understand it? But if we do say it, are they going to be overwhelmed by the words? We went one way in "Time's Arrow II," and maybe we tried too hard to explain things in "Realm of Fear," but it's hard to strike that back." (Captains' Logs: The Unauthorized Complete Trek Voyages)

Braga recalled, "I envisioned a scarier episode where the creatures in the transporter were a little more frightening, but then again what a tall order to the effects guys, 'Make it amorphous, but terrifying.' What does that mean? It's easy to write that, but difficult to visualize. I just wanted you to feel scared with this guy and you never really did." (Captains' Logs: The Unauthorized Complete Trek Voyages)